Structure of PDB 5yk2 Chain A Binding Site BS01

Receptor Information
>5yk2 Chain A (length=391) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKDEVTAELMEKAANQLFTVLGELKGGAMKVGQALSVMEAAIPDEFGEPY
REALTKLAPPLPASKVHRVLDGQLGTKWRERFSSFNDTPVASASIGQVHK
AIWSDGREVAVKIQYPGADEALRADLKTMQRMVGVLKQLSPGADVQGVVD
ELVERTEMELDYRLEAANQRAFAKAYHDHPRFQVPHVVASAPKVVIQEWI
EGVPMAEIIRHGTTEQRDLIGTLLAELTFDAPRRLGLMHGDAHPGNFMLL
PDGRMGIIDFGAVAPMPGGFPIELGMTIRLAREKNYDLLLPTMEKAGLIQ
RGRQVSVREIDEMLRQYVEPIQVEVFHYTRKWLQKMTVSQIDRTARQMDL
PAKLAIPMRVIASVGAILCQLDAHVPIKALSEELIPGFAEP
Ligand information
Ligand IDERY
InChIInChI=1S/C37H67NO13/c1-14-25-37(10,45)30(41)20(4)27(39)18(2)16-35(8,44)32(51-34-28(40)24(38(11)12)15-19(3)47-34)21(5)29(22(6)33(43)49-25)50-26-17-36(9,46-13)31(42)23(7)48-26/h18-26,28-32,34,40-42,44-45H,14-17H2,1-13H3/t18-,19-,20+,21+,22-,23+,24+,25-,26+,28-,29+,30-,31+,32-,34+,35-,36-,37-/m1/s1
InChIKeyULGZDMOVFRHVEP-RWJQBGPGSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C3OC(CC)C(O)(C)C(O)C(C(=O)C(C)CC(O)(C)C(OC1OC(C)CC(N(C)C)C1O)C(C(OC2OC(C(O)C(OC)(C2)C)C)C3C)C)C
OpenEye OEToolkits 1.5.0CCC1C(C(C(C(=O)C(CC(C(C(C(C(C(=O)O1)C)OC2CC(C(C(O2)C)O)(C)OC)C)OC3C(C(CC(O3)C)N(C)C)O)(C)O)C)C)O)(C)O
CACTVS 3.341CC[CH]1OC(=O)[CH](C)[CH](O[CH]2C[C](C)(OC)[CH](O)[CH](C)O2)[CH](C)[CH](O[CH]3O[CH](C)C[CH]([CH]3O)N(C)C)[C](C)(O)C[CH](C)C(=O)[CH](C)[CH](O)[C]1(C)O
CACTVS 3.341CC[C@H]1OC(=O)[C@H](C)[C@@H](O[C@H]2C[C@@](C)(OC)[C@@H](O)[C@H](C)O2)[C@H](C)[C@@H](O[C@@H]3O[C@H](C)C[C@@H]([C@H]3O)N(C)C)[C@](C)(O)C[C@@H](C)C(=O)[C@H](C)[C@@H](O)[C@]1(C)O
OpenEye OEToolkits 1.5.0CC[C@@H]1[C@@]([C@@H]([C@H](C(=O)[C@@H](C[C@@]([C@@H]([C@H]([C@@H]([C@H](C(=O)O1)C)O[C@H]2C[C@@]([C@H]([C@@H](O2)C)O)(C)OC)C)O[C@H]3[C@@H]([C@H](C[C@H](O3)C)N(C)C)O)(C)O)C)C)O)(C)O
FormulaC37 H67 N O13
NameERYTHROMYCIN A
ChEMBLCHEMBL532
DrugBankDB00199
ZINCZINC000085534336
PDB chain5yk2 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5yk2 Discovery of the first macrolide antibiotic binding protein in Mycobacterium tuberculosis: a new antibiotic resistance drug target.
Resolution2.807 Å
Binding residue
(original residue number in PDB)		E196 D286 A307 A309 I407 R410
Binding residue
(residue number reindexed from 1)		E151 D241 A262 A264 I356 R359
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Cellular Component
GO:0009274 peptidoglycan-based cell wall

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:5yk2, PDBe:5yk2, PDBj:5yk2
PDBsum5yk2
PubMed29350349
UniProtO53343

[Back to BioLiP]